Query psy6374
Match_columns 305
No_of_seqs 213 out of 1274
Neff 3.2
Searched_HMMs 46136
Date Sat Aug 17 00:51:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00191 60S ribosomal protein 100.0 2.7E-58 5.7E-63 395.3 14.3 141 164-305 5-145 (145)
2 KOG1751|consensus 100.0 7.7E-58 1.7E-62 396.6 11.6 147 159-305 9-157 (157)
3 PRK14548 50S ribosomal protein 100.0 1.2E-32 2.6E-37 218.0 9.6 84 222-305 1-84 (84)
4 TIGR03636 L23_arch archaeal ri 100.0 1.5E-30 3.2E-35 203.1 9.5 77 229-305 1-77 (77)
5 PRK05738 rplW 50S ribosomal pr 99.9 3.5E-26 7.5E-31 182.6 7.5 77 223-300 1-90 (92)
6 CHL00030 rpl23 ribosomal prote 99.9 2.5E-25 5.5E-30 179.0 7.8 76 223-300 1-89 (93)
7 PRK12280 rplW 50S ribosomal pr 99.9 3.3E-25 7.1E-30 193.2 7.5 79 220-300 1-92 (158)
8 COG0089 RplW Ribosomal protein 99.9 3.5E-25 7.6E-30 179.3 6.3 83 222-304 1-86 (94)
9 PF00276 Ribosomal_L23: Riboso 99.9 1.3E-23 2.8E-28 166.8 8.0 78 223-301 1-91 (91)
10 PF03939 Ribosomal_L23eN: Ribo 99.7 1.5E-19 3.3E-24 133.7 -1.0 53 165-217 2-54 (54)
11 KOG4089|consensus 95.0 0.032 6.9E-07 50.2 4.2 49 225-280 27-75 (165)
12 cd04929 ACT_TPH ACT domain of 72.1 5.7 0.00012 30.7 3.7 42 218-267 24-65 (74)
13 PF10298 WhiA_N: WhiA N-termin 59.6 23 0.00051 27.5 5.0 62 242-305 22-86 (86)
14 cd04931 ACT_PAH ACT domain of 57.1 15 0.00033 29.5 3.6 43 217-267 37-80 (90)
15 PF08777 RRM_3: RNA binding mo 56.2 26 0.00056 28.8 4.9 51 245-300 4-55 (105)
16 cd04904 ACT_AAAH ACT domain of 56.1 23 0.00051 26.6 4.3 43 217-267 23-65 (74)
17 PF03780 Asp23: Asp23 family; 54.5 17 0.00037 28.5 3.5 24 255-278 82-105 (108)
18 COG0089 RplW Ribosomal protein 52.3 6.7 0.00014 32.6 0.9 22 278-300 71-92 (94)
19 cd04930 ACT_TH ACT domain of t 49.6 28 0.0006 29.2 4.2 43 217-267 64-106 (115)
20 PLN02817 glutathione dehydroge 42.2 21 0.00045 33.4 2.6 39 264-302 24-62 (265)
21 PF01282 Ribosomal_S24e: Ribos 40.3 1.5E+02 0.0032 23.7 6.8 49 251-302 11-63 (84)
22 PRK01178 rps24e 30S ribosomal 40.0 1.3E+02 0.0028 25.1 6.7 69 230-302 5-81 (99)
23 cd01769 UBL Ubiquitin-like dom 38.3 72 0.0016 22.2 4.3 36 241-276 6-41 (69)
24 KOG3279|consensus 37.1 4 8.6E-05 39.1 -3.0 61 175-249 90-150 (283)
25 cd04880 ACT_AAAH-PDT-like ACT 36.9 60 0.0013 23.8 3.9 49 218-275 23-73 (75)
26 PLN03134 glycine-rich RNA-bind 35.6 84 0.0018 26.8 5.0 55 244-300 37-94 (144)
27 PF00240 ubiquitin: Ubiquitin 33.6 81 0.0018 22.6 4.0 36 242-277 5-40 (69)
28 PF14560 Ubiquitin_2: Ubiquiti 32.8 92 0.002 24.0 4.5 54 244-297 15-68 (87)
29 KOG3424|consensus 32.4 1.3E+02 0.0027 26.7 5.6 46 252-302 34-85 (132)
30 PRK04046 translation initiatio 29.3 96 0.0021 28.8 4.7 51 223-274 66-137 (222)
31 cd04905 ACT_CM-PDT C-terminal 28.5 76 0.0017 23.7 3.3 42 218-267 25-68 (80)
32 KOG0107|consensus 27.3 1.3E+02 0.0028 28.2 5.1 51 244-298 13-63 (195)
33 TIGR00323 eIF-6 translation in 24.8 1.5E+02 0.0033 27.6 5.1 50 222-273 103-175 (215)
34 smart00360 RRM RNA recognition 24.2 2.1E+02 0.0045 18.5 4.9 48 250-299 5-55 (71)
35 KOG2583|consensus 23.9 28 0.0006 35.9 0.2 14 5-18 160-173 (429)
36 PTZ00044 ubiquitin; Provisiona 23.9 1.6E+02 0.0034 21.6 4.2 36 241-276 9-44 (76)
37 PF00076 RRM_1: RNA recognitio 23.0 1.3E+02 0.0028 20.5 3.4 52 247-300 4-57 (70)
38 cd01809 Scythe_N Ubiquitin-lik 22.4 1.8E+02 0.004 20.7 4.2 37 241-277 9-45 (72)
39 smart00213 UBQ Ubiquitin homol 21.8 1.8E+02 0.0038 19.9 3.9 35 243-277 10-44 (64)
40 PF09581 Spore_III_AF: Stage I 21.6 2E+02 0.0044 24.8 5.1 40 254-293 88-133 (188)
41 TIGR02830 spore_III_AG stage I 21.4 97 0.0021 28.4 3.1 33 245-277 148-184 (186)
42 TIGR01661 ELAV_HUD_SF ELAV/HuD 21.4 1.9E+02 0.0042 26.7 5.2 57 242-302 270-331 (352)
43 PF01206 TusA: Sulfurtransfera 20.9 3.3E+02 0.0072 19.8 5.4 44 231-275 16-59 (70)
44 cd01796 DDI1_N DNA damage indu 20.5 1.5E+02 0.0033 22.1 3.6 34 241-274 8-41 (71)
No 1
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=100.00 E-value=2.7e-58 Score=395.34 Aligned_cols=141 Identities=62% Similarity=0.878 Sum_probs=137.5
Q ss_pred hhhhHHHHHHhhhhhcccCCCceeeeecccccCCCCcccCCCCCCCCCCCCCCCCCCCccccccccccchhhhhhhhcCC
Q psy6374 164 QGQVKKALKSKLKVLKGGHHTRTRKIRTSVRFHRPRTQRGGAAPKYMRRSVPRRNRMDAFNIIKYPLTTESAMKKIEDNN 243 (305)
Q Consensus 164 a~akaKAlKAkKaVlKG~hs~k~kKirts~~F~rPkTl~l~R~PKyprks~prrnklD~yaIIK~PLtTEKAmKkiEdnN 243 (305)
..++++|++|+++|++|+|+ +.+|||||++||||+||+|+|+|+|||+|+|++|+||+|+||++||+||++|+++|++|
T Consensus 5 ~~~~~ka~~a~k~~~~g~~~-~~~k~r~~~~f~rpktl~l~r~pky~r~~~~~~~~md~~~IIk~Pl~TEKa~~~~E~~N 83 (145)
T PTZ00191 5 KKAKKKAKKAAKAAKKGVKV-KKRKVRTSVRFFRPKTLRLPKKPKYPRRVKPASKKLDKYSIIKYPLTTEKAMKKIEDNN 83 (145)
T ss_pred chHHHHHHHHHHHHhccccc-ceeEeeecceecCCccccCCCCCCCcccccCCCCCCchhhhhhcccccHHHHHHHhhCC
Confidence 45778899999999999998 67999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhhhhCCC
Q psy6374 244 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKIGII 305 (305)
Q Consensus 244 tlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVANKIGii 305 (305)
+|||+||++|||+||++|||+||||+|.+|||||+|+|||||||+|.+|||||||||+||||
T Consensus 84 ~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~g~KKA~V~L~~~~~aidva~kiGi~ 145 (145)
T PTZ00191 84 TLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPDGLKKAYIRLSPDVDALDVANKIGII 145 (145)
T ss_pred EEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 99999999999999999999999999999999999999999999999999999999999997
No 2
>KOG1751|consensus
Probab=100.00 E-value=7.7e-58 Score=396.62 Aligned_cols=147 Identities=67% Similarity=0.921 Sum_probs=142.2
Q ss_pred CCCcchhhhHHHHHHhhhhhcccCCCceee-eecccccCCCCcccCCCCCCCCCCCCCCCCCCCcccc-ccccccchhhh
Q psy6374 159 LGKNEQGQVKKALKSKLKVLKGGHHTRTRK-IRTSVRFHRPRTQRGGAAPKYMRRSVPRRNRMDAFNI-IKYPLTTESAM 236 (305)
Q Consensus 159 ~~~~~a~akaKAlKAkKaVlKG~hs~k~kK-irts~~F~rPkTl~l~R~PKyprks~prrnklD~yaI-IK~PLtTEKAm 236 (305)
.+++.++++++||+++++|++|+|+|+.++ +|++++|+||.||+++|+|+|||+|.|+||+||||.| |+|||+||++|
T Consensus 9 pa~pka~a~akAlkakkav~kgv~~~~~~~~~~t~~~~~rP~t~~~~r~pk~prks~p~~~kld~y~~iik~plTtEsam 88 (157)
T KOG1751|consen 9 PAPPKAEAKAKALKAKKAVLKGVHSHKKKKKSRTSPTFRRPKTLDLTRAPKYPRKSPPRRPKLDHYAIIIKFPLTTESAM 88 (157)
T ss_pred CCCcchhhhHHHHHHHHHhhccccCCcccCCccccCCCCCCcccccccCccccccccCCCCcchhhhhHhccccchhhhh
Confidence 456778999999999999999999998866 9999999999999999999999999999999999877 89999999999
Q ss_pred hhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhhhhCCC
Q psy6374 237 KKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKIGII 305 (305)
Q Consensus 237 KkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVANKIGii 305 (305)
+++||||||||+||+++|||||+|||++|||++|.+|||||+|||+|||||+|++|||||||||+||||
T Consensus 89 Kk~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~kkayv~la~dydaldvankig~i 157 (157)
T KOG1751|consen 89 KKIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII 157 (157)
T ss_pred cchhhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCceeEEEecCCchhHHHHhcccccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999998
No 3
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=99.98 E-value=1.2e-32 Score=218.03 Aligned_cols=84 Identities=54% Similarity=0.896 Sum_probs=82.1
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhhh
Q psy6374 222 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANK 301 (305)
Q Consensus 222 ~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVANK 301 (305)
.|+||++|++||++|.++|++|+|+|+||.+|||.||++|||+||||+|.+|||||++.|||||||+|.+|++|+|||++
T Consensus 1 ~~~iI~~PviTEK~~~~~e~~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~k 80 (84)
T PRK14548 1 PYSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIASR 80 (84)
T ss_pred CccchhccccCHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHHh
Confidence 37899999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCC
Q psy6374 302 IGII 305 (305)
Q Consensus 302 IGii 305 (305)
|||+
T Consensus 81 ig~~ 84 (84)
T PRK14548 81 LGVF 84 (84)
T ss_pred hccC
Confidence 9996
No 4
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=99.97 E-value=1.5e-30 Score=203.11 Aligned_cols=77 Identities=53% Similarity=0.850 Sum_probs=75.8
Q ss_pred cccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhhhhCCC
Q psy6374 229 PLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKIGII 305 (305)
Q Consensus 229 PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVANKIGii 305 (305)
|++||++|.++|++|+|+|+||.+|||+||++|||.||||+|.+|||+|+++|||||||+|.+||+|+|||++|||+
T Consensus 1 P~iTEKs~~~~e~~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~KKA~VtL~~g~~a~~va~k~g~~ 77 (77)
T TIGR03636 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVKLAEEYAAEEIASRLGVF 77 (77)
T ss_pred CcccHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCceEEEEEECCCCcHHHHHHhhccC
Confidence 89999999999988999999999999999999999999999999999999999999999999999999999999996
No 5
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.93 E-value=3.5e-26 Score=182.56 Aligned_cols=77 Identities=39% Similarity=0.503 Sum_probs=73.5
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCC-------------CCeeeEEEEc
Q psy6374 223 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-------------DGKKKAYVRL 289 (305)
Q Consensus 223 yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrp-------------dG~KKAyV~L 289 (305)
|+||++|++||++|.++|++|+|+|+||+++||+||++|||+||||+|.+|||+|++ .+||||||+|
T Consensus 1 ~~ii~~P~~TEKs~~~~e~~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~~~g~~~~~KKA~VtL 80 (92)
T PRK05738 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRIGKRSDWKKAIVTL 80 (92)
T ss_pred CccccccccCHHHHHhHHhCCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecccccccCCcEEEEEEc
Confidence 579999999999999999899999999999999999999999999999999999999 6899999999
Q ss_pred CCCCcHHHHhh
Q psy6374 290 ARDYDALDVAN 300 (305)
Q Consensus 290 apDyDALDVAN 300 (305)
.+|++ ||+++
T Consensus 81 ~~g~~-i~~~~ 90 (92)
T PRK05738 81 AEGQK-IDFFG 90 (92)
T ss_pred CCCCE-Eeccc
Confidence 99998 88864
No 6
>CHL00030 rpl23 ribosomal protein L23
Probab=99.92 E-value=2.5e-25 Score=179.03 Aligned_cols=76 Identities=25% Similarity=0.420 Sum_probs=71.4
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCC-------------eeeEEEEc
Q psy6374 223 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG-------------KKKAYVRL 289 (305)
Q Consensus 223 yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG-------------~KKAyV~L 289 (305)
|+||++|++||++|.++| +|+|+|+||.+|||.||++|||.||||+|.+|||+|.+++ ||||||+|
T Consensus 1 ~~iI~~PivTEKs~~l~e-~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~~G~~~~~KKAiVtL 79 (93)
T CHL00030 1 MDGIKYPVFTDKSIRLLE-KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITL 79 (93)
T ss_pred CceeccceeCHHHHHhhH-CCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCcccccCCcEEEEEEc
Confidence 579999999999999996 6999999999999999999999999999999999999865 89999999
Q ss_pred CCCCcHHHHhh
Q psy6374 290 ARDYDALDVAN 300 (305)
Q Consensus 290 apDyDALDVAN 300 (305)
.+|++ ||++.
T Consensus 80 ~~g~~-I~~~~ 89 (93)
T CHL00030 80 QPGYS-IPLFR 89 (93)
T ss_pred CCcCE-ecccc
Confidence 99987 88874
No 7
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.91 E-value=3.3e-25 Score=193.25 Aligned_cols=79 Identities=35% Similarity=0.495 Sum_probs=74.8
Q ss_pred CCccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCC-------------CeeeEE
Q psy6374 220 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-------------GKKKAY 286 (305)
Q Consensus 220 lD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpd-------------G~KKAy 286 (305)
||+|+||++||+||++|.++| +|+|+|+||+++||+||++|||.||||+|.+|||||+++ +|||||
T Consensus 1 Md~~~iIk~PviTEKs~~l~e-~N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g~~~G~~~~~KKAi 79 (158)
T PRK12280 1 MNINEVIKKPILTEKSYSLMS-KNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRFPGFTNSYKKAY 79 (158)
T ss_pred CChHhhhhccccCHHHHhhhh-CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccCCcccccCCcEEEE
Confidence 899999999999999999988 589999999999999999999999999999999999886 799999
Q ss_pred EEcCCCCcHHHHhh
Q psy6374 287 VRLARDYDALDVAN 300 (305)
Q Consensus 287 V~LapDyDALDVAN 300 (305)
|+|.+|+. |||+.
T Consensus 80 VtL~~g~~-I~~f~ 92 (158)
T PRK12280 80 VTLAEGYS-INLFP 92 (158)
T ss_pred EECCCCCE-eeccC
Confidence 99999987 88864
No 8
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=3.5e-25 Score=179.26 Aligned_cols=83 Identities=42% Similarity=0.575 Sum_probs=74.4
Q ss_pred ccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEE---cCCCCcHHHH
Q psy6374 222 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVR---LARDYDALDV 298 (305)
Q Consensus 222 ~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~---LapDyDALDV 298 (305)
+|+||++|++||++|.++|++|+|||+||.+|||.||++|||.||||+|.+|||||++++.|++++. +..+|++.+|
T Consensus 1 ~~dvI~~PvvTEKa~~l~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k~~G~~~~~kka~V 80 (94)
T COG0089 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYV 80 (94)
T ss_pred CcchhhcceecHHHHHhHhhCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEeccccccCcccceeEE
Confidence 5899999999999999998889999999999999999999999999999999999999877777775 7777777777
Q ss_pred hhhhCC
Q psy6374 299 ANKIGI 304 (305)
Q Consensus 299 ANKIGi 304 (305)
+.++|.
T Consensus 81 ~l~~G~ 86 (94)
T COG0089 81 TLKEGQ 86 (94)
T ss_pred EccCCC
Confidence 766664
No 9
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=99.89 E-value=1.3e-23 Score=166.77 Aligned_cols=78 Identities=41% Similarity=0.617 Sum_probs=71.2
Q ss_pred cccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCC-----CC--------eeeEEEEc
Q psy6374 223 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-----DG--------KKKAYVRL 289 (305)
Q Consensus 223 yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrp-----dG--------~KKAyV~L 289 (305)
|+||++|++||++|.++|++|+|+|+||+++||+||+++||+||||+|.+|||+|++ .| ||||||+|
T Consensus 1 ~~ii~~p~iTeKs~~~~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKaiVtL 80 (91)
T PF00276_consen 1 YDIIKKPVITEKSMKLLENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKAIVTL 80 (91)
T ss_dssp TTTEEEE--SHHHHHHHHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEEEEEE
T ss_pred CCEeecceecHhHHHhhhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEEEEEe
Confidence 789999999999999999989999999999999999999999999999999999998 34 59999999
Q ss_pred CCCCcHHHHhhh
Q psy6374 290 ARDYDALDVANK 301 (305)
Q Consensus 290 apDyDALDVANK 301 (305)
.+| +.+|++++
T Consensus 81 ~~~-~~i~~~~~ 91 (91)
T PF00276_consen 81 KEG-DKIPLFEE 91 (91)
T ss_dssp STT-SCHHHHHT
T ss_pred CCC-CccccccC
Confidence 999 56999864
No 10
>PF03939 Ribosomal_L23eN: Ribosomal protein L23, N-terminal domain; InterPro: IPR005633 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a.; PDB: 3IZR_X 4A1E_R 4A1A_R 4A1C_R 4A17_R 3O5H_W 3IZS_X 3O58_W.
Probab=99.74 E-value=1.5e-19 Score=133.75 Aligned_cols=53 Identities=58% Similarity=0.792 Sum_probs=17.5
Q ss_pred hhhHHHHHHhhhhhcccCCCceeeeecccccCCCCcccCCCCCCCCCCCCCCC
Q psy6374 165 GQVKKALKSKLKVLKGGHHTRTRKIRTSVRFHRPRTQRGGAAPKYMRRSVPRR 217 (305)
Q Consensus 165 ~akaKAlKAkKaVlKG~hs~k~kKirts~~F~rPkTl~l~R~PKyprks~prr 217 (305)
+++++|++|+++||+|+|+++.++||||++|+||+||+|+|+|+|||+|+|+|
T Consensus 2 ~a~~KA~kakKav~KG~~~~~~rKirts~~F~rPKTL~l~R~PKYprkS~p~r 54 (54)
T PF03939_consen 2 KAKAKALKAKKAVLKGVHSKKKRKIRTSVTFRRPKTLRLPRQPKYPRKSVPRR 54 (54)
T ss_dssp ----------------------HHHHHHHHHT-SS--------SS-SSS---S
T ss_pred chHHHHHHHHHHHhcCCCccccceeecCcccCCCcccccCCCCCCcccCCCCC
Confidence 46778999999999999999989999999999999999999999999999986
No 11
>KOG4089|consensus
Probab=94.96 E-value=0.032 Score=50.20 Aligned_cols=49 Identities=24% Similarity=0.419 Sum_probs=41.7
Q ss_pred cccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCC
Q psy6374 225 IIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD 280 (305)
Q Consensus 225 IIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpd 280 (305)
+|..|+.+. -.|+.+|+|+...||++|+.....+||..|.+|.|++..+
T Consensus 27 ~l~rp~~~q-------~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~G 75 (165)
T KOG4089|consen 27 NLVRPLVTQ-------PPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHG 75 (165)
T ss_pred hhhcccccC-------CCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeec
Confidence 344477764 2478999999999999999999999999999999998664
No 12
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=72.11 E-value=5.7 Score=30.65 Aligned_cols=42 Identities=7% Similarity=0.138 Sum_probs=32.4
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhC
Q psy6374 218 NRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYD 267 (305)
Q Consensus 218 nklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYd 267 (305)
+.++...|--+|... .+..|.|.||+..+..+|+++++.|=.
T Consensus 24 ~~inl~~IeSRP~~~--------~~~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 24 LGINVVHIESRKSKR--------RSSEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred CCCCEEEEEeccCCC--------CCceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 455666777777554 235799999999999999999998743
No 13
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=59.64 E-value=23 Score=27.49 Aligned_cols=62 Identities=18% Similarity=0.364 Sum_probs=22.4
Q ss_pred CCeEEEEEeeCCCH--HHHHHHHHHHhCCceeeEEeeeCCC-CeeeEEEEcCCCCcHHHHhhhhCCC
Q psy6374 242 NNTLVFIVHLQANK--HHIKAAVKKMYDINVAKVNTLIRPD-GKKKAYVRLARDYDALDVANKIGII 305 (305)
Q Consensus 242 nNtlVFiVDvkANK--~QIKqAVKKLYdVkVaKVNTLIrpd-G~KKAyV~LapDyDALDVANKIGii 305 (305)
++.+++.+...-.- .-|-.-++++||+++ .|.+..... +....|+-.-+|. +.++..++||+
T Consensus 22 ~~~~~l~~~ten~~vARri~~llk~~f~i~~-ei~v~~~~~l~k~~~Y~i~i~~~-~~~iL~~lgll 86 (86)
T PF10298_consen 22 NGRISLEISTENAAVARRIYSLLKKLFDIDP-EISVRRSRNLKKNNVYTIRIEDS-AKEILRDLGLL 86 (86)
T ss_dssp TTEEEE--EES-HHHHHHHHHHHHHTT--EE-EEEEEE-SSSBEEE---------------------
T ss_pred CCEEEEEEEeCCHHHHHHHHHHHHHHhCCCe-EEEEecCCCCCCCCccccccccc-cccccccccCC
Confidence 56777766665333 678889999999988 444443222 2234444333333 78899999985
No 14
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=57.05 E-value=15 Score=29.51 Aligned_cols=43 Identities=12% Similarity=0.285 Sum_probs=32.8
Q ss_pred CCCCCccccccccccchhhhhhhhcCCeEEEEEeeCCC-HHHHHHHHHHHhC
Q psy6374 217 RNRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQAN-KHHIKAAVKKMYD 267 (305)
Q Consensus 217 rnklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkAN-K~QIKqAVKKLYd 267 (305)
...++...|.-+|..++ ...|+|.||+..+ ...++++++.|-.
T Consensus 37 ~~~INLt~IeSRP~~~~--------~~~Y~FfVDieg~~~~~~~~~l~~L~~ 80 (90)
T cd04931 37 EKDINLTHIESRPSRLN--------KDEYEFFINLDKKSAPALDPIIKSLRN 80 (90)
T ss_pred HCCCCEEEEEeccCCCC--------CceEEEEEEEEcCCCHHHHHHHHHHHH
Confidence 45677778888886542 3679999999986 7888888888743
No 15
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=56.18 E-value=26 Score=28.77 Aligned_cols=51 Identities=25% Similarity=0.381 Sum_probs=28.9
Q ss_pred EEEE-EeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhh
Q psy6374 245 LVFI-VHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVAN 300 (305)
Q Consensus 245 lVFi-VDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVAN 300 (305)
|-|. ++...++.+|+..|.. |+ +|.-|.. ..|...+||+|....+|-.+..
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yVD~---~~G~~~g~VRf~~~~~A~~a~~ 55 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYVDF---SRGDTEGYVRFKTPEAAQKALE 55 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEEE-----TT-SEEEEEESS---HHHHHH
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceEEe---cCCCCEEEEEECCcchHHHHHH
Confidence 4466 7788899999999998 55 5655554 4588899999998877655544
No 16
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=56.11 E-value=23 Score=26.61 Aligned_cols=43 Identities=9% Similarity=0.193 Sum_probs=33.2
Q ss_pred CCCCCccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhC
Q psy6374 217 RNRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYD 267 (305)
Q Consensus 217 rnklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYd 267 (305)
.+.++...|--+|+..+ ...|.|.||+..+..+++++++.|-.
T Consensus 23 ~~~iNlt~IeSRP~~~~--------~~~y~Ffvd~~~~~~~~~~~l~~L~~ 65 (74)
T cd04904 23 EFGVNLTHIESRPSRRN--------GSEYEFFVDCEVDRGDLDQLISSLRR 65 (74)
T ss_pred HCCCcEEEEECCCCCCC--------CceEEEEEEEEcChHHHHHHHHHHHH
Confidence 34566777778886642 35799999999988889999988754
No 17
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=54.50 E-value=17 Score=28.48 Aligned_cols=24 Identities=33% Similarity=0.541 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhCCceeeEEeeeC
Q psy6374 255 KHHIKAAVKKMYDINVAKVNTLIR 278 (305)
Q Consensus 255 K~QIKqAVKKLYdVkVaKVNTLIr 278 (305)
..+|+++|+.+.|++|..||..+.
T Consensus 82 q~~V~~~v~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 82 QEKVKEAVEEMTGIEVSEVNVHVE 105 (108)
T ss_pred HHHHHHHHHHHHCCeeEEEEEEEE
Confidence 578999999999999999999873
No 18
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=52.26 E-value=6.7 Score=32.57 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=18.7
Q ss_pred CCCCeeeEEEEcCCCCcHHHHhh
Q psy6374 278 RPDGKKKAYVRLARDYDALDVAN 300 (305)
Q Consensus 278 rpdG~KKAyV~LapDyDALDVAN 300 (305)
+..+||+|||+|..|+. ||+++
T Consensus 71 ~~~~~kka~V~l~~G~~-i~~~~ 92 (94)
T COG0089 71 LRKDYKKAYVTLKEGQS-IDFFG 92 (94)
T ss_pred cCcccceeEEEccCCCE-Eeecc
Confidence 45689999999999998 88764
No 19
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=49.63 E-value=28 Score=29.18 Aligned_cols=43 Identities=7% Similarity=0.176 Sum_probs=32.9
Q ss_pred CCCCCccccccccccchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhC
Q psy6374 217 RNRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYD 267 (305)
Q Consensus 217 rnklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYd 267 (305)
.+.++...|--+|+-+ .+..|.|.||+..+..++.++++.|-.
T Consensus 64 ~~gINLt~IESRP~~~--------~~~eY~FfIdieg~~~~~~~aL~~L~~ 106 (115)
T cd04930 64 TFEAKIHHLESRPSRK--------EGGDLEVLVRCEVHRSDLLQLISSLRQ 106 (115)
T ss_pred HCCCCEEEEECCcCCC--------CCceEEEEEEEEeCHHHHHHHHHHHHH
Confidence 3456667777777544 246799999999999999999988753
No 20
>PLN02817 glutathione dehydrogenase (ascorbate)
Probab=42.18 E-value=21 Score=33.38 Aligned_cols=39 Identities=15% Similarity=0.269 Sum_probs=34.5
Q ss_pred HHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHHhhhh
Q psy6374 264 KMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANKI 302 (305)
Q Consensus 264 KLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDVANKI 302 (305)
.-|++.+..+|++.+++|+++++|++....+.|+|+.|-
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (265)
T PLN02817 24 PRFGTSHGGAKGVKRVGGRRRKYLTAITMSSPLEVCVKA 62 (265)
T ss_pred ccccceeecccccccCCcccceeEEecCCCccHHHHHhc
Confidence 457888899999999999999999999999999998764
No 21
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=40.33 E-value=1.5e+02 Score=23.75 Aligned_cols=49 Identities=14% Similarity=0.356 Sum_probs=31.5
Q ss_pred eCCCHHHHHHHHHHHhCCceeeE--EeeeCCC--CeeeEEEEcCCCCcHHHHhhhh
Q psy6374 251 LQANKHHIKAAVKKMYDINVAKV--NTLIRPD--GKKKAYVRLARDYDALDVANKI 302 (305)
Q Consensus 251 vkANK~QIKqAVKKLYdVkVaKV--NTLIrpd--G~KKAyV~LapDyDALDVANKI 302 (305)
..-+|.+|+..+-.+||++...| +.+...- |.-..|..+ ||.+|.+.++
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~I---Yd~~e~~kk~ 63 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKI---YDSAEALKKF 63 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEE---ESSHHHHHHH
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEE---eCCHHHHHHh
Confidence 34589999999999999876544 5555554 345666666 4555555543
No 22
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=39.99 E-value=1.3e+02 Score=25.06 Aligned_cols=69 Identities=19% Similarity=0.341 Sum_probs=43.5
Q ss_pred ccchhhhhhhhcCCeEEEEEeeC----CCHHHHHHHHHHHhCCceeeEEe--eeCC--CCeeeEEEEcCCCCcHHHHhhh
Q psy6374 230 LTTESAMKKIEDNNTLVFIVHLQ----ANKHHIKAAVKKMYDINVAKVNT--LIRP--DGKKKAYVRLARDYDALDVANK 301 (305)
Q Consensus 230 LtTEKAmKkiEdnNtlVFiVDvk----ANK~QIKqAVKKLYdVkVaKVNT--LIrp--dG~KKAyV~LapDyDALDVANK 301 (305)
++.++...++. ..+++|.|.-. -+|.+|+..+-++|+.+..-|=. +..- .|.=..|+.+ ||.+|.+.+
T Consensus 5 I~~~~~N~LL~-Rke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv~~~~t~fG~g~s~G~a~I---Yds~e~~kk 80 (99)
T PRK01178 5 IISDKENPLLG-RREIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVRKIKTEYGMGKSKGYAKV---YDDKERARK 80 (99)
T ss_pred EEEeeecCCcC-cEEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEEEccCccCCCceEEEEEEE---ECCHHHHHh
Confidence 34556666665 46888988643 58999999999999976544322 1111 2444455544 566777665
Q ss_pred h
Q psy6374 302 I 302 (305)
Q Consensus 302 I 302 (305)
+
T Consensus 81 ~ 81 (99)
T PRK01178 81 I 81 (99)
T ss_pred h
Confidence 4
No 23
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=38.31 E-value=72 Score=22.17 Aligned_cols=36 Identities=11% Similarity=0.109 Sum_probs=31.3
Q ss_pred cCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEee
Q psy6374 241 DNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 276 (305)
Q Consensus 241 dnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTL 276 (305)
+.+.+.|.|+...+=.++|+.|...+++.+..+..+
T Consensus 6 ~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~ 41 (69)
T cd01769 6 TGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLI 41 (69)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE
Confidence 457888999999999999999999999988887663
No 24
>KOG3279|consensus
Probab=37.07 E-value=4 Score=39.07 Aligned_cols=61 Identities=26% Similarity=0.382 Sum_probs=39.7
Q ss_pred hhhhcccCCCceeeeecccccCCCCcccCCCCCCCCCCCCCCCCCCCccccccccccchhhhhhhhcCCeEEEEE
Q psy6374 175 LKVLKGGHHTRTRKIRTSVRFHRPRTQRGGAAPKYMRRSVPRRNRMDAFNIIKYPLTTESAMKKIEDNNTLVFIV 249 (305)
Q Consensus 175 KaVlKG~hs~k~kKirts~~F~rPkTl~l~R~PKyprks~prrnklD~yaIIK~PLtTEKAmKkiEdnNtlVFiV 249 (305)
.+|.||-...-..|.| -++||-|+ .|+++-...-||.| ..-++||.+|.+|++..-|-|++
T Consensus 90 e~vikg~~~~~~tk~~-~p~~wvp~----------l~~~v~~s~ild~y---~~v~vteRtl~LIDE~~GLD~YI 150 (283)
T KOG3279|consen 90 EAVIKGFQKREQTKRR-VPHFWVPN----------LRRSVVHSHVLDCY---MSVVVTERTLELIDECHGLDHYI 150 (283)
T ss_pred HHHHHHHHHHHHHhhc-CCcccccc----------hhhHHHHHHHHhhh---heeeehHHHHHHHHHhcCcceee
Confidence 3566664332222222 68899887 34566666667776 34468999999998877777665
No 25
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=36.91 E-value=60 Score=23.82 Aligned_cols=49 Identities=14% Similarity=0.253 Sum_probs=32.4
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEeeCC--CHHHHHHHHHHHhCCceeeEEe
Q psy6374 218 NRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQA--NKHHIKAAVKKMYDINVAKVNT 275 (305)
Q Consensus 218 nklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkA--NK~QIKqAVKKLYdVkVaKVNT 275 (305)
..++...|.-+|... ....|.|.||+.. +..++.++++.|=+. +..|++
T Consensus 23 ~~vni~~I~Srp~~~--------~~~~~~f~id~~~~~~~~~~~~~l~~l~~~-~~~~~~ 73 (75)
T cd04880 23 RGINLTKIESRPSRK--------GLWEYEFFVDFEGHIDDPDVKEALEELKRV-TEDVKV 73 (75)
T ss_pred CCCCEEEEEeeecCC--------CCceEEEEEEEECCCCCHHHHHHHHHHHHh-CCeeEE
Confidence 345555666666443 3467999999998 588888888877442 334443
No 26
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=35.57 E-value=84 Score=26.82 Aligned_cols=55 Identities=9% Similarity=0.238 Sum_probs=37.3
Q ss_pred eEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCC-C--eeeEEEEcCCCCcHHHHhh
Q psy6374 244 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD-G--KKKAYVRLARDYDALDVAN 300 (305)
Q Consensus 244 tlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpd-G--~KKAyV~LapDyDALDVAN 300 (305)
-||=-++..++-.+|++.|+. || .|..|..+..+. | .-=+||++....+|....+
T Consensus 37 lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~ 94 (144)
T PLN03134 37 LFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94 (144)
T ss_pred EEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHH
Confidence 344446667889999999987 66 677777765442 2 1239999997777655544
No 27
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=33.60 E-value=81 Score=22.59 Aligned_cols=36 Identities=11% Similarity=0.126 Sum_probs=32.2
Q ss_pred CCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeee
Q psy6374 242 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 277 (305)
Q Consensus 242 nNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLI 277 (305)
..+|.|.|+...+=.++|+.|...+|+.+.....+-
T Consensus 5 g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~ 40 (69)
T PF00240_consen 5 GKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY 40 (69)
T ss_dssp SEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE
T ss_pred CcEEEEEECCCCCHHHhhhhcccccccccccceeee
Confidence 458999999999999999999999999998887664
No 28
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=32.84 E-value=92 Score=23.98 Aligned_cols=54 Identities=13% Similarity=0.145 Sum_probs=39.4
Q ss_pred eEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHH
Q psy6374 244 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALD 297 (305)
Q Consensus 244 tlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALD 297 (305)
.+...++...+=.|+|+-++.+||+.+.......+.+..-.-++.|..|...|.
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~ 68 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLG 68 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCC
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEee
Confidence 445677888899999999999999999999998884322245667766555443
No 29
>KOG3424|consensus
Probab=32.37 E-value=1.3e+02 Score=26.73 Aligned_cols=46 Identities=28% Similarity=0.379 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhCCceeeEEeeeC---CCCee---eEEEEcCCCCcHHHHhhhh
Q psy6374 252 QANKHHIKAAVKKMYDINVAKVNTLIR---PDGKK---KAYVRLARDYDALDVANKI 302 (305)
Q Consensus 252 kANK~QIKqAVKKLYdVkVaKVNTLIr---pdG~K---KAyV~LapDyDALDVANKI 302 (305)
..+|.||++-+-+||.++...|-.+-- -+|.+ .+.| ||.||++.++
T Consensus 34 ~vsK~EirEKla~mYkt~~d~V~vfgfrt~~GggkstgfalI-----Ydsve~akkf 85 (132)
T KOG3424|consen 34 NVSKTEIREKLAKMYKTTPDAVFVFGFRTHFGGGKSTGFALI-----YDSVEYAKKF 85 (132)
T ss_pred CCCHHHHHHHHHHHhcCCcceEEEEEeeeccCCcccceeeee-----eehHHHHHhc
Confidence 578999999999999887655544321 12322 3444 8899999875
No 30
>PRK04046 translation initiation factor IF-6; Provisional
Probab=29.27 E-value=96 Score=28.79 Aligned_cols=51 Identities=12% Similarity=0.214 Sum_probs=40.4
Q ss_pred cccccccccchhhhhhhhcC---------------------CeEEEEEeeCCCHHHHHHHHHHHhCCceeeEE
Q psy6374 223 FNIIKYPLTTESAMKKIEDN---------------------NTLVFIVHLQANKHHIKAAVKKMYDINVAKVN 274 (305)
Q Consensus 223 yaIIK~PLtTEKAmKkiEdn---------------------NtlVFiVDvkANK~QIKqAVKKLYdVkVaKVN 274 (305)
+-+|..|.+++..++.+++. |-+.++|++..+..+++ .+++.+||+|....
T Consensus 66 ~g~lvp~~~~~~e~~~l~e~L~v~V~~~~~~~~~vGn~i~~N~~G~lv~p~~~~ee~~-~i~~~L~V~v~~~t 137 (222)
T PRK04046 66 NGILVPSIVLDEELELLKEALDLNVEVLPSKLTALGNLILANDKGALVHPELSDEARK-VIEDTLGVEVERGT 137 (222)
T ss_pred ceEEeCCCCCHHHHHHHHHhcCceEEEEeccccceEeEEEEcCcEEEECCCCCHHHHH-HHHHhhCceEEEEe
Confidence 45667788888887777654 66789999999999998 58888899887665
No 31
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=28.50 E-value=76 Score=23.69 Aligned_cols=42 Identities=12% Similarity=0.236 Sum_probs=28.8
Q ss_pred CCCCccccccccccchhhhhhhhcCCeEEEEEeeCCC--HHHHHHHHHHHhC
Q psy6374 218 NRMDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQAN--KHHIKAAVKKMYD 267 (305)
Q Consensus 218 nklD~yaIIK~PLtTEKAmKkiEdnNtlVFiVDvkAN--K~QIKqAVKKLYd 267 (305)
+.++...|..+|.-. ++..|+|.||...+ ..++.++++.|=+
T Consensus 25 ~~ini~~i~s~p~~~--------~~~~~~f~vd~~~~~~~~~~~~~l~~l~~ 68 (80)
T cd04905 25 RGINLTKIESRPSKG--------GLWEYVFFIDFEGHIEDPNVAEALEELKR 68 (80)
T ss_pred CCcCEEEEEEEEcCC--------CCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 345555666666422 34679999999985 7888888887644
No 32
>KOG0107|consensus
Probab=27.26 E-value=1.3e+02 Score=28.24 Aligned_cols=51 Identities=27% Similarity=0.303 Sum_probs=40.2
Q ss_pred eEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCCCeeeEEEEcCCCCcHHHH
Q psy6374 244 TLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDV 298 (305)
Q Consensus 244 tlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpdG~KKAyV~LapDyDALDV 298 (305)
.||=-...+++|.+|..+|-. || .+-+|.+-..|.|+ |||.+..--||.|-
T Consensus 13 VYVGnL~~~a~k~eLE~~F~~-yG-~lrsvWvArnPPGf--AFVEFed~RDA~DA 63 (195)
T KOG0107|consen 13 VYVGNLGSRATKRELERAFSK-YG-PLRSVWVARNPPGF--AFVEFEDPRDAEDA 63 (195)
T ss_pred EEeccCCCCcchHHHHHHHHh-cC-cceeEEEeecCCCc--eEEeccCcccHHHH
Confidence 455556778999999887755 55 67788888889997 99999988887774
No 33
>TIGR00323 eIF-6 translation initiation factor eIF-6, putative. This model finds translation initiation factor eIF-6 of eukaryotes, which is a ribosome dissociation factor. It also finds a set of apparent archaeal orthologs, slightly shorter proteins not yet shown to act as initiation factors; these probably should be designated as translation initiation factor aIF-6, putative.
Probab=24.77 E-value=1.5e+02 Score=27.57 Aligned_cols=50 Identities=14% Similarity=0.201 Sum_probs=33.8
Q ss_pred ccccccccccchhhhhhhhc-----------------------CCeEEEEEeeCCCHHHHHHHHHHHhCCceeeE
Q psy6374 222 AFNIIKYPLTTESAMKKIED-----------------------NNTLVFIVHLQANKHHIKAAVKKMYDINVAKV 273 (305)
Q Consensus 222 ~yaIIK~PLtTEKAmKkiEd-----------------------nNtlVFiVDvkANK~QIKqAVKKLYdVkVaKV 273 (305)
-+-+|.+|.+++...+.+++ || ..-+|+++.+..+++. ++.+|||+|..-
T Consensus 103 d~G~lv~~~~~~~e~~~i~~~L~v~V~~~~i~~~~~vG~~~v~nN-~G~lvhP~~s~ee~~~-i~d~LgV~v~~g 175 (215)
T TIGR00323 103 DYGALASPELDRDTEELISDVLGVEVFRGTIAGLITVGSYAVVTN-RGGLVHPQTSVQEQEE-LSSLLGVELVAG 175 (215)
T ss_pred CceEEeCCCCCHHHHHHHHHhcCCcEEEEecccccccceEEEEeC-cEEEECCCCCHHHHHH-HHHHhCCcEEEE
Confidence 34566666666666655542 34 4457888888888874 788888887655
No 34
>smart00360 RRM RNA recognition motif.
Probab=24.23 E-value=2.1e+02 Score=18.53 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=30.8
Q ss_pred eeCCCHHHHHHHHHHHhCCceeeEEeeeCCC---CeeeEEEEcCCCCcHHHHh
Q psy6374 250 HLQANKHHIKAAVKKMYDINVAKVNTLIRPD---GKKKAYVRLARDYDALDVA 299 (305)
Q Consensus 250 DvkANK~QIKqAVKKLYdVkVaKVNTLIrpd---G~KKAyV~LapDyDALDVA 299 (305)
+...+..+|++.++. || .|..|+.+..+. ..--+||++....+|....
T Consensus 5 ~~~~~~~~l~~~f~~-~g-~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~ 55 (71)
T smart00360 5 PPDVTEEELRELFSK-FG-KIESVRLVRDKDTGKSKGFAFVEFESEEDAEKAL 55 (71)
T ss_pred CcccCHHHHHHHHHh-hC-CEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHH
Confidence 445688899998876 55 455666665443 1236999997665554443
No 35
>KOG2583|consensus
Probab=23.93 E-value=28 Score=35.88 Aligned_cols=14 Identities=50% Similarity=0.947 Sum_probs=12.0
Q ss_pred ccchhhhccccccc
Q psy6374 5 PIHRATFRNSLGDK 18 (305)
Q Consensus 5 ~~~~~~~~~~~~~~ 18 (305)
-||+++|||.||..
T Consensus 160 ~lH~aAfRngLgns 173 (429)
T KOG2583|consen 160 QLHAAAFRNGLGNS 173 (429)
T ss_pred HHHHHHHhcccCCc
Confidence 48999999999974
No 36
>PTZ00044 ubiquitin; Provisional
Probab=23.86 E-value=1.6e+02 Score=21.60 Aligned_cols=36 Identities=14% Similarity=0.252 Sum_probs=31.8
Q ss_pred cCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEee
Q psy6374 241 DNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 276 (305)
Q Consensus 241 dnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTL 276 (305)
+.+++++.|+...+=.+||+-|+..+|+.+.....+
T Consensus 9 ~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 44 (76)
T PTZ00044 9 TGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI 44 (76)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE
Confidence 457999999999999999999999999988877655
No 37
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=22.99 E-value=1.3e+02 Score=20.52 Aligned_cols=52 Identities=12% Similarity=0.158 Sum_probs=33.7
Q ss_pred EEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCCC--CeeeEEEEcCCCCcHHHHhh
Q psy6374 247 FIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPD--GKKKAYVRLARDYDALDVAN 300 (305)
Q Consensus 247 FiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrpd--G~KKAyV~LapDyDALDVAN 300 (305)
=-++.+.+..+|++.+..+=+| ..+....... ...-+||++....+|..+..
T Consensus 4 ~nlp~~~t~~~l~~~f~~~g~i--~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~ 57 (70)
T PF00076_consen 4 GNLPPDVTEEELRDFFSQFGKI--ESIKVMRNSSGKSKGYAFVEFESEEDAEKALE 57 (70)
T ss_dssp ESETTTSSHHHHHHHHHTTSTE--EEEEEEEETTSSEEEEEEEEESSHHHHHHHHH
T ss_pred cCCCCcCCHHHHHHHHHHhhhc--ccccccccccccccceEEEEEcCHHHHHHHHH
Confidence 3356778999999999994344 3444443222 34568999987777655543
No 38
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=22.43 E-value=1.8e+02 Score=20.70 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=31.5
Q ss_pred cCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeee
Q psy6374 241 DNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 277 (305)
Q Consensus 241 dnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLI 277 (305)
+.+++.|.|+...+=.++|+.|...+|+.+.....+.
T Consensus 9 ~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 9 DSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 3468999999999999999999999999887765553
No 39
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=21.79 E-value=1.8e+02 Score=19.92 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=29.9
Q ss_pred CeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeee
Q psy6374 243 NTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLI 277 (305)
Q Consensus 243 NtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLI 277 (305)
.++.|.|+...+=.++|+.|...+++.+.....+.
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 47889999999999999999999999887766553
No 40
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=21.59 E-value=2e+02 Score=24.80 Aligned_cols=40 Identities=30% Similarity=0.383 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHhCCceeeEEeeeCCCC------eeeEEEEcCCCC
Q psy6374 254 NKHHIKAAVKKMYDINVAKVNTLIRPDG------KKKAYVRLARDY 293 (305)
Q Consensus 254 NK~QIKqAVKKLYdVkVaKVNTLIrpdG------~KKAyV~LapDy 293 (305)
=..||+.-++..||+.+.+|..-+.-+. -++..|+|.++.
T Consensus 88 l~~~i~~~l~~~~g~~~~~V~v~~~~~~~~~~~~I~~I~v~l~~~~ 133 (188)
T PF09581_consen 88 LEKQIKALLEDKYGVEVVKVEVEIDEDEESPDFEIKEIKVTLSEEE 133 (188)
T ss_pred HHHHHHHHHhhhcCCceEEEEEEEEcCCCccccceeEEEEEEcCCC
Confidence 4578888899899999999999887663 578889998854
No 41
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=21.40 E-value=97 Score=28.45 Aligned_cols=33 Identities=33% Similarity=0.359 Sum_probs=26.2
Q ss_pred EEEEEeeCCC----HHHHHHHHHHHhCCceeeEEeee
Q psy6374 245 LVFIVHLQAN----KHHIKAAVKKMYDINVAKVNTLI 277 (305)
Q Consensus 245 lVFiVDvkAN----K~QIKqAVKKLYdVkVaKVNTLI 277 (305)
=|.+|--.+. |.+|-+||..||||...+|+.+=
T Consensus 148 GVlVVAeGa~~~~Vk~~I~~AV~~ll~v~~hkI~V~~ 184 (186)
T TIGR02830 148 GVLVVAEGAENPQIKYRIVEAVSRVLDVPAHKVSVLP 184 (186)
T ss_pred EEEEEeeCCCCHHHHHHHHHHHHHHhCCCcceEEEEe
Confidence 4566666665 57778899999999999999873
No 42
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=21.38 E-value=1.9e+02 Score=26.65 Aligned_cols=57 Identities=11% Similarity=0.145 Sum_probs=0.0
Q ss_pred CCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEeeeCC-----CCeeeEEEEcCCCCcHHHHhhhh
Q psy6374 242 NNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP-----DGKKKAYVRLARDYDALDVANKI 302 (305)
Q Consensus 242 nNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNTLIrp-----dG~KKAyV~LapDyDALDVANKI 302 (305)
.+-||+-+....+-.+|++.+.. || .|..|+.+..+ .|+ +||.+..-.+|......+
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~~-fG-~v~~v~i~~d~~t~~skG~--aFV~F~~~~~A~~Ai~~l 331 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFGP-FG-AVQNVKIIRDLTTNQCKGY--GFVSMTNYDEAAMAILSL 331 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHh-CC-CeEEEEEeEcCCCCCccce--EEEEECCHHHHHHHHHHh
No 43
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=20.86 E-value=3.3e+02 Score=19.76 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=35.3
Q ss_pred cchhhhhhhhcCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEEe
Q psy6374 231 TTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNT 275 (305)
Q Consensus 231 tTEKAmKkiEdnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVNT 275 (305)
.+-++++.++.+..|.+++|-.....+|...++.. |..+..++.
T Consensus 16 ~~~~~l~~l~~G~~l~v~~d~~~~~~di~~~~~~~-g~~~~~~~~ 59 (70)
T PF01206_consen 16 KAKKALKELPPGEVLEVLVDDPAAVEDIPRWCEEN-GYEVVEVEE 59 (70)
T ss_dssp HHHHHHHTSGTT-EEEEEESSTTHHHHHHHHHHHH-TEEEEEEEE
T ss_pred HHHHHHHhcCCCCEEEEEECCccHHHHHHHHHHHC-CCEEEEEEE
Confidence 35667777877778999999999999999999885 767777765
No 44
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=20.52 E-value=1.5e+02 Score=22.06 Aligned_cols=34 Identities=15% Similarity=0.126 Sum_probs=29.7
Q ss_pred cCCeEEEEEeeCCCHHHHHHHHHHHhCCceeeEE
Q psy6374 241 DNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVN 274 (305)
Q Consensus 241 dnNtlVFiVDvkANK~QIKqAVKKLYdVkVaKVN 274 (305)
..+++++.|+...+=.++|+.|...+||.+....
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~ 41 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQ 41 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeE
Confidence 4578999999999999999999999999886653
Done!